A lot of people with just a week would choose 2 nights in Heraklio & 5 in Chania. Don't try to see all of Crete in a week! But in Heraklio you'll want to see Knossos & the archaeological museum (even if you're not big museum fans).
If you don't want to spend a couple of night on the South coast, then if you stay in Chania for the rest of your stay you can visit lots of superb places on daytrips. You could stop in Rethymno for a few hours on the journey to Chania.
Imbros is a very pleasant drive, up into the hills & you can easily DIY it - leave your car at the top of the gorge (just after the far end of the village), & then at the bottom of the gorge - takes around 2 1/2 hours or so to walk - at Komitades you can get a 'taxi', usually the back of a pick-up truck for an adrenaline filled drive back up, or if you have time, go down to Sfakia, where there are lovely fish tavernas next to the water. you may be able to co-incide with a bus back to your car.
If the weather is good you could do a day to Elafonisi, via Topolia gorge with its cave church, back via the coastline. Don't expect it to be sunbathing weather, but it could be perfect for walking on the beach - do wade over to the island to see the pink sand. Maybe brave members of your party could swim (cold!).
Aptera will be incredible when you come, as it is already absolutely filled with wildflowers, it's a natural, organic place, with very interesting roman water cisterns, bathhouses, post-Minoan house ruins, monastery & a newly restored amplitheatre set in an ancient olive grove.
You might ike to see the 3 monasteries of Akrotiri, to the North of Chania - the first, Agia Triada is an imposing, impressive, building, worth a look round & very photogenic, from there it's a short, fascinating drive to the 2nd monastery & then the walk down to the 3rd, Katholiko is fabulous! around 1 1/2 hours there & back.
I'd suggest you stay in the old town of Chania, near the Venetian harbour. It will be very safe for your boys to explore on their own, & the area is full of great restaurants. Plenty of hotels in quirky renovated Venetian houses, to suit all budgets.